Author: tlinnet
Date: Thu May 8 12:43:56 2014
New Revision: 23076
URL: http://svn.gna.org/viewcvs/relax?rev=23076&view=rev
Log:
Made systemtest Relax_disp.test_cpmg_synthetic_dx_map_points to start testing.
Modified also sample CPMG script to allow for this.
task #7791: (https://gna.org/task/index.php?7791 ) the dx.map should accept a
list of list with values for points.
Modified:
trunk/test_suite/system_tests/relax_disp.py
trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=23076&r1=23075&r2=23076&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Thu May 8 12:43:56 2014
@@ -1223,6 +1223,129 @@
## Make test on parameters. Only if breaking the
relative change.
self.assertAlmostEqual(set_val, min_val, 1)
+
+
+ def test_cpmg_synthetic_dx_map_points(self):
+ """Test synthetic cpmg data, calling the dx.map function with one or
two points.
+
+ This script will produce synthetic CPMG R2eff values according to
the selected model, and the fit the selected model.
+ """
+
+ # Reset.
+ #self.interpreter.reset()
+
+ ## Set Experiments.
+ model_create = MODEL_NS_CPMG_2SITE_EXPANDED
+ model_analyse = 'CR72'
+ # Exp 1
+ sfrq_1 = 599.8908617*1E6
+ r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1)
+ time_T2_1 = 0.06
+ ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60]
+ r2eff_err_1 = [0, 0, 0, 0, 0, 0, 0, 0]
+ exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_err_1]
+
+ sfrq_2 = 499.8908617*1E6
+ r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2)
+ time_T2_2 = 0.05
+ ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50]
+ r2eff_err_2 = [0, 0, 0, 0, 0, 0, 0, 0]
+ exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_err_2]
+
+ # Collect all exps
+ exps = [exp_1, exp_2]
+
+ spins = [
+ ['Ala', 1, 'N', {'r2': {r20_key_1:2, r20_key_2:2}, 'r2a':
{r20_key_1:2, r20_key_2:2}, 'r2b': {r20_key_1:2, r20_key_2:2}, 'kex': 1000,
'pA': 0.99, 'dw': 2} ]
+ ]
+
+ # Collect the data to be used.
+ ds.data = [model_create, model_analyse, spins, exps]
+
+ # The tmp directory. None is the local directory.
+ ds.tmpdir = ds.tmpdir
+
+ # The results directory. None is the local directory.
+ #ds.resdir = None
+ ds.resdir = ds.tmpdir
+
+ # Do set_grid_r20_from_min_r2eff ?.
+ ds.set_grid_r20_from_min_r2eff = True
+
+ # Remove insignificant level.
+ ds.insignificance = 0.0
+
+ # The grid search size (the number of increments per dimension).
+ ds.GRID_INC = None
+
+ # The do clustering.
+ ds.do_cluster = False
+
+ # The function tolerance. This is used to terminate minimisation
once the function value between iterations is less than the tolerance.
+ # The default value is 1e-25.
+ ds.set_func_tol = 1e-9
+
+ # The maximum number of iterations.
+ # The default value is 1e7.
+ ds.set_max_iter = 1000
+
+ # The verbosity level.
+ ds.verbosity = 1
+
+ # The rel_change WARNING level.
+ ds.rel_change = 0.05
+
+ # The plot_curves.
+ ds.plot_curves = False
+
+ # The conversion for ShereKhan at http://sherekhan.bionmr.org/.
+ ds.sherekhan_input = False
+
+ # Make a dx map to be opened om OpenDX. To map the hypersurface of
chi2, when altering kex, dw and pA.
+ ds.opendx = False
+
+ # The set r2eff err.
+ ds.r2eff_err = 0.1
+
+ # The print result info.
+ ds.print_res = False
+
+ # Execute the script.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'cpmg_synthetic.py')
+
+ # Get the spins.
+ cur_spins = ds.data[2]
+
+ # First switch pipe, since dx.map will go through parameters and end
up a "bad" place. :-)
+ ds.pipe_name_MODEL_MAP = "%s_%s_map"%(ds.pipe_name, model_analyse)
+ self.interpreter.pipe.copy(pipe_from=ds.pipe_name ,
pipe_to=ds.pipe_name_MODEL_MAP, bundle_to = ds.pipe_bundle)
+ self.interpreter.pipe.switch(pipe_name=ds.pipe_name_MODEL_MAP)
+
+ # Copy R2eff, but not the original parameters
+ self.interpreter.value.copy(pipe_from=ds.pipe_name_r2eff,
pipe_to=ds.pipe_name_MODEL_MAP, param='r2eff')
+
+ # Then select model.
+ self.interpreter.relax_disp.select_model(model=model_analyse)
+
+ # Define dx.map settings.
+ ds.dx_inc = 4
+ ds.dx_params = ['dw', 'pA', 'kex']
+
+ # First loop over the defined spins and set the model parameters.
+ for i in range(len(cur_spins)):
+ res_name, res_num, spin_name, params = cur_spins[i]
+ cur_spin_id = ":%i@%s"%(res_num, spin_name)
+ cur_spin = return_spin(cur_spin_id)
+
+ print("Params for dx map is")
+ print(ds.dx_params)
+ print("Point param for dx map is")
+ print(ds.dx_set_val)
+ cur_model = model_analyse.replace(' ', '_')
+ file_name_map = "%s_map%s" % (cur_model,
cur_spin_id.replace('#', '_').replace(':', '_').replace('@', '_'))
+ file_name_point = "%s_point%s" % (cur_model, cur_spin_id
.replace('#', '_').replace(':', '_').replace('@', '_'))
+ self.interpreter.dx.map(params=ds.dx_params, map_type='Iso3D',
spin_id=cur_spin_id, inc=ds.dx_inc, lower=None, upper=None, axis_incs=10,
file_prefix=file_name_map, dir=ds.resdir, point=[ds.dx_set_val,
ds.dx_clust_val], point_file=file_name_point, remap=None)
+ #self.interpreter.dx.map(params=ds.dx_params, map_type='Iso3D',
spin_id=cur_spin_id, inc=ds.dx_inc, lower=None, upper=None, axis_incs=10,
file_prefix=file_name_map, dir=ds.resdir, point=ds.dx_set_val,
point_file=file_name_point, remap=None)
def test_curve_type_cpmg_fixed_time(self):
Modified: trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py?rev=23076&r1=23075&r2=23076&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
(original)
+++ trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py Thu
May 8 12:43:56 2014
@@ -99,13 +99,13 @@
exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2]
# Collect all exps
- #exps = [exp_1, exp_2]
- exps = [exp_1]
+ exps = [exp_1, exp_2]
+ #exps = [exp_1]
# Add more spins here.
spins = [
- ['Ala', 1, 'N', {'r2': {r20_key_1: 20.0, r20_key_2: 20.0},
'r2a': {r20_key_1: 20.0, r20_key_2: 20.0}, 'r2b': {r20_key_1: 20.0,
r20_key_2: 20.0}, 'kex': 2200.0, 'pA': 0.993, 'dw': 1.5} ]
- #['Ala', 2, 'N', {'r2': {r20_key_1: 13.0, r20_key_2: 14.5},
'r2a': {r20_key_1: 13.0, r20_key_2: 14.5}, 'r2b': {r20_key_1: 13.0,
r20_key_2: 14.5}, 'kex': 2200.0, 'pA': 0.993, 'dw': 1.5} ]
+ ['Ala', 1, 'N', {'r2': {r20_key_1: 25.0, r20_key_2: 24.0},
'r2a': {r20_key_1: 25.0, r20_key_2: 24.0}, 'r2b': {r20_key_1: 25.0,
r20_key_2: 24.0}, 'kex': 2200.0, 'pA': 0.993, 'dw': 1.5} ]
+ #['Ala', 2, 'N', {'r2': {r20_key_1: 15.0, r20_key_2: 14.0},
'r2a': {r20_key_1: 15.0, r20_key_2: 14.0}, 'r2b': {r20_key_1: 15.0,
r20_key_2: 14.0}, 'kex': 2200.0, 'pA': 0.993, 'dw': 1.5} ]
]
ds.data = [model_create, model_analyse, spins, exps]
@@ -165,9 +165,10 @@
# To map the hypersurface of chi2, when altering kex, dw and pA.
if not hasattr(ds, 'opendx'):
ds.opendx = True
-
if not hasattr(ds, 'dx_inc'):
- ds.dx_inc = 50
+ ds.dx_inc = 4
+if not hasattr(ds, 'dx_params'):
+ ds.dx_params = ['dw', 'pA', 'kex']
# The set r2eff err.
if not hasattr(ds, 'r2eff_err'):
@@ -189,11 +190,11 @@
model_analyse = ds.data[1]
# Create the data pipe.
-pipe_name = 'base pipe'
-pipe_type = 'relax_disp'
-pipe_bundle = 'relax_disp'
-pipe_name_r2eff = "%s_%s_R2eff"%(model_create, pipe_name)
-pipe.create(pipe_name=pipe_name, pipe_type=pipe_type, bundle = pipe_bundle)
+ds.pipe_name = 'base pipe'
+ds.pipe_type = 'relax_disp'
+ds.pipe_bundle = 'relax_disp'
+ds.pipe_name_r2eff = "%s_%s_R2eff"%(model_create, ds.pipe_name )
+pipe.create(pipe_name=ds.pipe_name , pipe_type=ds.pipe_type, bundle =
ds.pipe_bundle)
# Generate the sequence.
cur_spins = ds.data[2]
@@ -217,7 +218,6 @@
for ncyc in ncycs:
nu_cpmg = ncyc / time_T2
cur_id = '%s_%.1f' % (exp_id, nu_cpmg)
- print cur_id
ids.append(cur_id)
# Set the spectrometer frequency.
@@ -235,35 +235,35 @@
print("\n\nThe experiment IDs are %s." % ids)
## Now prepare to calculate the synthetic R2eff values.
-pipe.copy(pipe_from=pipe_name, pipe_to=pipe_name_r2eff, bundle_to =
pipe_bundle)
-pipe.switch(pipe_name=pipe_name_r2eff)
+pipe.copy(pipe_from=ds.pipe_name , pipe_to=ds.pipe_name_r2eff, bundle_to =
ds.pipe_bundle)
+pipe.switch(pipe_name=ds.pipe_name_r2eff)
# Then select model.
relax_disp.select_model(model=model_create)
-# First loop over the spins and set the model parameters.
-for res_name, res_num, spin_name, params in cur_spins:
+# First loop over the defined spins and set the model parameters.
+for i in range(len(cur_spins)):
+ res_name, res_num, spin_name, params = cur_spins[i]
cur_spin_id = ":%i@%s"%(res_num, spin_name)
cur_spin = return_spin(cur_spin_id)
- #print cur_spin.model, cur_spin.name, cur_spin.isotope
-
- #print as
- # Now set the parameters.
+
+ if ds.print_res:
+ print("For spin: '%s'"%cur_spin_id)
for mo_param in cur_spin.params:
# The R2 is a dictionary, depending on spectrometer frequency.
if isinstance(getattr(cur_spin, mo_param), dict):
set_r2 = params[mo_param]
- for key, val in set_r2.items():
+ for key, val in getattr(cur_spin, mo_param).items():
# Update value to float
set_r2.update({ key : float(val) })
- print cur_spin.model, res_name, cur_spin_id, mo_param, key,
float(val)
+ print(cur_spin.model, res_name, cur_spin_id, mo_param, key,
float(val))
+ # Set it back
setattr(cur_spin, mo_param, set_r2)
else:
before = getattr(cur_spin, mo_param)
setattr(cur_spin, mo_param, float(params[mo_param]))
after = getattr(cur_spin, mo_param)
- print cur_spin.model, res_name, cur_spin_id, mo_param, before
-
+ print(cur_spin.model, res_name, cur_spin_id, mo_param, before)
## Now doing the back calculation of R2eff values.
@@ -326,51 +326,14 @@
print("Did following number of iterations: %i"%i)
-# Do a dx map.
-# To map the hypersurface of chi2, when altering kex, dw and pA.
-if ds.opendx:
- # First switch pipe, since dx.map will go through parameters and end up
a "bad" place. :-)
- pipe_name_MODEL_MAP = "%s_%s_map"%(pipe_name, model_analyse)
- pipe.copy(pipe_from=pipe_name, pipe_to=pipe_name_MODEL_MAP, bundle_to =
pipe_bundle)
- pipe.switch(pipe_name=pipe_name_MODEL_MAP)
-
- # Copy R2eff, but not the original parameters
- value.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL_MAP,
param='r2eff')
-
- # Then select model.
- relax_disp.select_model(model=model_analyse)
-
- # Define dx parameters
- dx_params = ['dw', 'pA', 'kex']
- for res_name, res_num, spin_name, params in cur_spins:
- cur_spin_id = ":%i@%s"%(res_num, spin_name)
- cur_spin = return_spin(cur_spin_id)
- dx_point = []
-
- # Now get the parameters.
- for dx_param in dx_params:
- set_value = float(params[dx_param ])
- dx_point.append(set_value)
-
- print("Params for dx map is")
- print(dx_params)
- print("Point param for dx map is")
- print(dx_point)
- file_name_map = "map%s" % (cur_spin_id .replace('#',
'_').replace(':', '_').replace('@', '_'))
- file_name_point = "point%s" % (cur_spin_id .replace('#',
'_').replace(':', '_').replace('@', '_'))
- dx.map(params=dx_params, map_type='Iso3D', spin_id=cur_spin_id,
inc=ds.dx_inc, lower=None, upper=None, axis_incs=5,
file_prefix=file_name_map, dir=ds.resdir, point=dx_point,
point_file=file_name_point, remap=None)
- #vp_exec: A flag specifying whether to execute the visual program
automatically at start-up.
- #dx.execute(file_prefix=file_name, dir=ds.resdir, dx_exe='dx',
vp_exec=True)
-
-# Now do fitting.
-
+### Now do fitting.
# Change pipe.
-pipe_name_MODEL = "%s_%s"%(pipe_name, model_analyse)
-pipe.copy(pipe_from=pipe_name, pipe_to=pipe_name_MODEL, bundle_to =
pipe_bundle)
-pipe.switch(pipe_name=pipe_name_MODEL)
+ds.pipe_name_MODEL = "%s_%s"%(ds.pipe_name , model_analyse)
+pipe.copy(pipe_from=ds.pipe_name , pipe_to=ds.pipe_name_MODEL, bundle_to =
ds.pipe_bundle)
+pipe.switch(pipe_name=ds.pipe_name_MODEL)
# Copy R2eff, but not the original parameters
-value.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL, param='r2eff')
+value.copy(pipe_from=ds.pipe_name_r2eff, pipe_to=ds.pipe_name_MODEL,
param='r2eff')
# Then select model.
relax_disp.select_model(model=model_analyse)
@@ -427,12 +390,12 @@
# Now do clustering
if ds.do_cluster:
# Change pipe.
- pipe_name_MODEL_CLUSTER = "%s_%s_CLUSTER"%(pipe_name, model_create)
- pipe.copy(pipe_from=pipe_name, pipe_to=pipe_name_MODEL_CLUSTER)
- pipe.switch(pipe_name=pipe_name_MODEL_CLUSTER)
+ ds.pipe_name_MODEL_CLUSTER = "%s_%s_CLUSTER"%(ds.pipe_name ,
model_create)
+ pipe.copy(pipe_from=ds.pipe_name , pipe_to=ds.pipe_name_MODEL_CLUSTER)
+ pipe.switch(pipe_name=ds.pipe_name_MODEL_CLUSTER)
# Copy R2eff, but not the original parameters
- value.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL_CLUSTER,
param='r2eff')
+ value.copy(pipe_from=ds.pipe_name_r2eff,
pipe_to=ds.pipe_name_MODEL_CLUSTER, param='r2eff')
# Then select model.
relax_disp.select_model(model=model_create)
@@ -441,7 +404,7 @@
relax_disp.cluster('model_cluster', ":1-100")
# Copy the parameters from before.
- relax_disp.parameter_copy(pipe_from=pipe_name_MODEL,
pipe_to=pipe_name_MODEL_CLUSTER)
+ relax_disp.parameter_copy(pipe_from=ds.pipe_name_MODEL,
pipe_to=ds.pipe_name_MODEL_CLUSTER)
# Now minimise.
minimise(min_algor='simplex', func_tol=ds.set_func_tol,
max_iter=ds.set_max_iter, constraints=True, scaling=True,
verbosity=ds.verbosity)
@@ -468,16 +431,21 @@
print("Analysing with MODEL:%s."%(model_analyse))
print("########################\n")
+# Looping over data, to collect the results.
+# Define which dx_params to collect for.
+ds.dx_set_val = list(range(len(ds.dx_params)))
+ds.dx_clust_val = list(range(len(ds.dx_params)))
for i in range(len(cur_spins)):
res_name, res_num, spin_name, params = cur_spins[i]
cur_spin_id = ":%i@%s"%(res_num, spin_name)
cur_spin = return_spin(cur_spin_id)
+ # Fetch data.
grid_params = ds.grid_results[i][3]
min_params = ds.min_results[i][3]
clust_params = ds.clust_results[i][3]
+
# Now read the parameters.
-
if ds.print_res:
print("For spin: '%s'"%cur_spin_id)
for mo_param in cur_spin.params:
@@ -514,3 +482,41 @@
print("###################################")
print("WARNING: %s Have relative change above %.2f, and
is %.4f."%(mo_param, ds.rel_change, rel_change))
print("###################################\n")
+
+ # Store to dx map.
+ if mo_param in ds.dx_params:
+ ds.dx_set_val[ds.dx_params.index(mo_param)] = set_val
+ ds.dx_clust_val[ds.dx_params.index(mo_param)] = clust_val
+
+## Do a dx map.
+# To map the hypersurface of chi2, when altering kex, dw and pA.
+if ds.opendx:
+ # First switch pipe, since dx.map will go through parameters and end up
a "bad" place. :-)
+ ds.pipe_name_MODEL_MAP = "%s_%s_map"%(ds.pipe_name, model_analyse)
+ pipe.copy(pipe_from=ds.pipe_name , pipe_to=ds.pipe_name_MODEL_MAP,
bundle_to = ds.pipe_bundle)
+ pipe.switch(pipe_name=ds.pipe_name_MODEL_MAP)
+
+ # Copy R2eff, but not the original parameters
+ value.copy(pipe_from=ds.pipe_name_r2eff, pipe_to=ds.pipe_name_MODEL_MAP,
param='r2eff')
+
+ # Then select model.
+ relax_disp.select_model(model=model_analyse)
+
+ # First loop over the defined spins and set the model parameters.
+ for i in range(len(cur_spins)):
+ res_name, res_num, spin_name, params = cur_spins[i]
+ cur_spin_id = ":%i@%s"%(res_num, spin_name)
+ cur_spin = return_spin(cur_spin_id)
+
+ if ds.print_res:
+ print("Params for dx map is")
+ print(ds.dx_params)
+ print("Point param for dx map is")
+ print(ds.dx_set_val)
+ cur_model = model_analyse.replace(' ', '_')
+ file_name_map = "%s_map%s" % (cur_model, cur_spin_id.replace('#',
'_').replace(':', '_').replace('@', '_'))
+ file_name_point = "%s_point%s" % (cur_model, cur_spin_id
.replace('#', '_').replace(':', '_').replace('@', '_'))
+ #dx.map(params=ds.dx_params, map_type='Iso3D', spin_id=cur_spin_id,
inc=ds.dx_inc, lower=None, upper=None, axis_incs=10,
file_prefix=file_name_map, dir=ds.resdir, point=[ds.dx_set_val,
ds.dx_clust_val], point_file=file_name_point, remap=None)
+ dx.map(params=ds.dx_params, map_type='Iso3D', spin_id=cur_spin_id,
inc=ds.dx_inc, lower=None, upper=None, axis_incs=10,
file_prefix=file_name_map, dir=ds.resdir, point=ds.dx_set_val,
point_file=file_name_point, remap=None)
+ #vp_exec: A flag specifying whether to execute the visual program
automatically at start-up.
+ #dx.execute(file_prefix=file_name, dir=ds.resdir, dx_exe='dx',
vp_exec=True)
r23076 - in /trunk/test_suite/system_tests: relax_disp.py scripts/relax_disp/cpmg_synthetic.py